1. Field of the Invention
The present invention relates to the DNA coding for phosphoserine phosphatase of coryneform bacteria. The DNA may be utilized for microbiologic industry, such as breeding L-serine producing coryneform bacteria.
2. Description of the Related Art
As a conventional method of producing L-serine by fermentation, there has been reported the method in which a bacterial strain capable of converting glycine and sugar into L-serine is used in a mediumcontaining 30 g/L of glycine to produce at most 14 g/L of L-serine. The conversion yield amounted to 46% (Kubota, K., Agricultural Biological Chemistry, 49, 7-12 (1985)). Using a bacterial strain capable of converting glycine and methanol into L-serine, 53 g/L of L-serine can be produced from 100 g/L of glycine (T. Yoshida et al., Journal of Fermentation and Bioengineering, Vol. 79, No. 2, 181-183, 1995). In the method using Nocardia, it has been known that the L-serine productivity of the bacterium can be improved by breeding those strains resistant to serine hydroxamate, azaserine or the like (Japanese Patent Publication No. 57-1235). However, these methods involve use of glycine that is a precursor of L-serine and include complicated operation and is disadvantageous from the viewpoint of costs.
As strains that can ferment L-serine directly from a sugar and do not need addition of the precursor of L-serine to the medium, there has been known Corynebacterium glutamicum that is resistant to D-serine, xc3xa1-methylserine, o-methylserine, isoserine, serine hydroxamate, and 3-chloroalanine but the accumulation of L-serine is as low as 0.8 g/L (Nogei Kagakukaishi, Vol. 48, No. 3, p.201-208, 1974). Accordingly, further strain improvements are needed for direct fermentation of L-serine on an industrial scale.
On the other hand, regarding coryneform bacteria, there have been disclosed a vector plasmid that is capable of autonomous replication in the cell and having a drug resistance marker gene (cf. U.S. Pat. No. 4,514,502) and a method of introducing a gene into the cell (Japanese Patent Application Laid-open No. 2-207791). These techniques have been utilized for breeding L-amino acid producing bacteria. As for L-serine, it has been found that L-serine productivity of coryneform bacteria having the L-serine producing ability is improved by introduction of a gene coding for D-3-phosphoglyceratedehydrogenase whose feedback inhibition by L-serine is desensitized (serA gene) (European Patent Application Laid-Open No. 943687), or amplification of a gene coding for phosphoserine phosphatase (serB) or phosphoserine transaminase (serC) (European Patent Application Laid-Open No. 931833). There has been known serB gene in Escherichia coli (GenBank accession X03046, M30784), Yeast (GenBank accession U36473), Helicobacter pylori (GenBank accession AF006039), however, serB gene of coryneform bacteria has not been known.
An object of the present invention, in view of the aforementioned points, is to provide the DNA coding for phosphoserine phosphatase of coryneform bacteria.
The present inventors obtained the DNA fragment from a chromosome DNA library of Brevibacterium flavum, which complimented serB deficiency of Escherichia coli. The open reading frame having homology with known serB gene of Escherichia coli was subcloned from the DNA fragment and introduced into serB deficient mutant strain of aforementioned Escherichia coli. However, serB deficiency was not complemented. It was found that serB deficiency was complemented with the aforementioned ORF which was forcedly expressed utilizing lac promoter. Thus, it was confirmed that the aforementioned ORF was serB homologue of Brevibacterium flavum. It was indicated that the aforementioned ORF did not have its own promoter because of forming operon.
The present invention was accomplished as described above, and provides the followings.
(1) A protein defined in the following (A) or (B):
(A) A protein which comprises an amino acid sequence of SEQ ID: 2 in Sequence Listing; or
(B) A protein which comprises an amino acid sequence including substitution, deletion, insertion, addition or inversion of one or several amino acids in the amino acid sequence of SEQ ID NO: 2 in Sequence Listing, and which has phosphoserine phosphatase activity.
(2) A DNA coding for a protein as defined in the following (A) or (B):
(A) A protein which comprises an amino acid sequence of SEQ ID: 2 in Sequence Listing; or
(B) A protein which comprises an amino acid sequence including substitution, deletion, insertion, addition or inversion of one or several amino acids in the amino acid sequence of SEQ ID NO: 2 in Sequence Listing, and which has phosphoserine phosphatase activity.
(3) A DNA coding for a protein having phosphoserine phosphatase activity which hybridizes under stringent conditions to a DNA sequence encoding a protien which comprises an amino acid sequence of SEQ ID NO: 2.
(4) The DNA according to (3), the stringent conditions comprise washing at 60xc2x0 C. and at a salt concentration corresponding to 1xc3x97SSC and 0.1% SDS.
(5) The DNA according to (2), which is DNA as defined in the following (a) or (b):
(a) A DNA which comprises a nucleotide sequence corresponding to nucleotide numbers of 210-1547 of nucleotide sequence of SEQ NO: 1 in Sequence Listing; or
(b) A DNA which is hybridizable with a probe which comprises the nucleotide sequence corresponding to nucleotide numbers of 210-1547 of nucleotide sequence of SEQ NO: 13 in Sequence Listing or a partial nucleotide sequence under stringent conditions, and which codes for the protein having the phosphoserine phosphatase activity.
(6) The DNA according to (5), the stringent conditions comprise washing at 60xc2x0 C. and at a salt concentration corresponding to 1xc3x97SSC and 0.1% SDS.
(7) A vector comprising the DNA according to any of (1) to (6).
(8) A bacterial cell in which phosphoserine phosphate activity encoded by the DNA according to any of (1) to (16) is increased.
(9) A method of producing L-serine comprising the steps of cultivating the bacterium according to (8) ina medium to produce and accumulate L-serine in the medium, and collecting L-serine from the medium.
Hereafter, the present invention will be explained in detail.
The DNA of the present invention can be obtained through PCR (polymerase chain reaction) utilizing chromosomal DNA of Brevibacterium flavum, for example, the Brevibacterium flavum strain ATCC14067, as a template, as well as a primer having the nucleotide sequence of SEQ ID NOs: 3 and 4 shown in sequence listing. Because each of these primers has a restriction enzyme recognition site of EcoRI or SalI in their 5xe2x80x2 sequences, the amplification product digested with these restriction enzymes can be inserted into a vector having EcoRI and SalI digested ends.
The nucleotide sequences of the aforementioned primers were designed based on the nucleotide sequence of the DNA fragment which complements serB deficient mutant strain Escherichia coli ME8320 (thi, serB, zhi-1::Tn10) (available from national genetics institute). By using these primers, a DNA fragment containing the coding region of the serB homologue and its flanking region (5xe2x80x2 non-translation region of about 200 bp and 3xe2x80x2 non-translation region of about 300 bp) can be obtained.
The nucleotide sequence of the coding region of the DNA of the present invention obtained as described above and an amino acid sequence which may be encoded by the sequence are shown in SEQ ID NO: 1. The amino acid sequence alone is shown in SEQ ID NO: 2.
The aforementioned serB homologue was found as the open reading frame (ORF) having homology with serB genes of Escherichia coli and Yeast (Saccharomyces cerevisiae), which existed in the DNA fragment complementing serB deficiency of strain ME8320. The DNA fragment having enough length to contain the ORF and the promoter was obtained from Brevibacterium flavum ATCC14067 by PCR utilizing aforementioned primers having the nucleotide sequence of SEQ ID NOs: 3 and 4 shown in sequence listing. It was introduced into strain ME8320, however the serB deficiency of the strain was not complemented. Therefore, at first, it was thought that the aforementioned ORF was not serB homologue. However, the serB deficiency was complemented with the aforementioned ORF which was ligated to lac promoter and forcedly expressed. Thus, it was confirmed that the aforementioned ORF was serB homologue.
Further, the other ORF wag found just upstream of serB homologue in the DNA fragment that compliments serB deficiency. From these results, it was indicated that these ORFs form a operon and there was no promoter region and the like just upstream of serf homologue.
At first, it was attempted to obtain serB homologue of Brevibacterium flavum utilizing nucleotide sequence of known serB gene. That is, the inventors intended to compare nucleotide sequence and amino acid sequence of known serB gene among the other species, to search highly conserved amino acid sequence region among various species, to synthesize PCR primers based on the nucleotide sequence of the region and to amplify serB homologue with these primers. However, since there were few such conserved regions, they estimated that it was difficult to obtain the objective gene by PCR. Therefore, complementation test utilizing serB deficient mutant strain was performed.
While the DNA of the present invention was obtained by cloning by complementation test utilizing serB deficient mutannt and subcloning by PCR as described above, it can also be obtained from a chromosome DNA library of Brevibacterium flavum by hybridization utilizing an oligonucleotide as a probe prepared based on the nucleotide sequence of the DNA of the present invention.
Methods for construction of genomic DNA library, hybridization, PCR, preparation of plasmid DNA, digestion and ligation of DNA, transformation and the like are described in Sambrook, J., Fritsch, and E. F., Maniatis, T., Molecular Cloning, Cold Spring Harbor Laboratory Press, 1.21 (1989).
The DNA of the present invention may encode phosphoserine phosphatase including substitution, deletion, insertion, addition, or inversion of one or several amino acids at one or a plurality of positions, provided that the activity of phosphoserine phosphatase encoded thereby is not deteriorated. Although the number of xe2x80x9cseveralxe2x80x9d amino acids differs depending on the position or the type of amino acid residues in the three-dimensional structure of the protein, it may be 2 to 200, preferably 2 to 50, and more preferably 2 to 20.
Further, the DNA of the present invention may encode phosphoserine phosphatase having homology of not less than 50%, preferably not less than 60% more preferably not less than 70%, further preferably not less than 80%, and most preferably not less than 90% with the amino acid sequence of SEQ ID NO: 2, provided that the activity of phosphoserine phosphatase encoded thereby is not deteriorated.
DNA, which encodes the substantially same protein as phosphoserine phosphatase as described above, is obtained, for example, by modifying the nucleotide sequence of phosphoserine phosphatase gene, for example, by means of the site-directed mutagenesis method so that one or more amino acid residues at a specified site of the gene involve substitution, deletion, insertion, addition, or inversion. DNA modified as described above may be obtained by the conventionally known mutation treatment. The mutation treatment includes a method for treating DNA coding for phosphoserine phosphatase in vitro, for example, with hydroxylamine, and a method for treating a microorganism, for example, a bacterium belonging to the genus Escherichia harboring DNA encoding phosphoserine phosphatase with ultraviolet irradiation or a mutating agent such as N-methyl-Nxe2x80x2-nitro-N-nitrosoguanidine (NTG) and nitrous acid usually used for the mutation treatment.
The substitution, deletion, insertion, addition, or inversion of nucleotide as described above also includes mutation (mutant or variant) which naturally occurs, for example, the difference in strains, species or genera of the microorganism.
The DNA, which codes for substantially the same protein as phosphoserine phosphatase, is obtained by expressing DNA having mutation as described above in an appropriate cell, and investigating the phosphoserine phosphatase activity of an expressed product. The DNA, which codes for substantially the same protein as phosphoserine phosphatase, is also obtained by isolating DNA which is hybridizable with a primer having, for example, the nucleotide sequence comprise the nucleotide numbers of 210-1547 of the nucleotide sequence of SEQ ID NO:1, under stringent conditions, and which codes for a protein having the phosphoserine phosphatase activity, from DNA coding for phosphoserine phosphatase having mutation or from a cell harboring it. The xe2x80x9cstringent conditionsxe2x80x9d referred to herein are conditions under which so-called specific hybrid is formed, and non-specific hybrid is not formed. It is difficult to clearly express this condition by using any numerical value. However, for example, the stringent conditions include conditions under which DNA""s having high homology, for example, DNA""s having homology of not less than 50% are hybridized with each other, and DNA""s having homology lower than the above are not hybridized with each other. Alternatively, the stringent conditions are exemplified by conditions which comprise ordinary condition of washing in Southern hybridization, e.g., 60xc2x0 C., 1xc3x97SSC, 0.1% SDS, preferably 0.1xc3x97SSC, 0.1% SDS.
DNA which has homology of not less than 60%, preferably not less than 70%, more preferably not less than 80%, and most preferably not less than 90% with the nucleotide sequence of SEQ ID NO: 1, and encodes a protein having the activity of phosphoserine phosphatase is included in the DNA of the present invention.
As a probe, a partial sequence of the nucleotide sequence of SEQ ID NO: 1 can also be used. Such a probe may be prepared by PCR using oligonucleotides produced based on the nucleotide sequence of SEQ ID NO: 1 as primers, and a DNA fragment containing the nucleotide sequence of SEQ ID NO: 1 as a template. When a DNA fragment in a length of about 300 bp is used as the probe, the conditions of washing for the hybridization consist of, for example, 50xc2x0 C., 2xc3x97SSC, and 0.1% SDS.
The gene, which is hybridizable under the condition as described above, includes those having a stop codon generated in the gene, and those having no activity due to mutation of active center. However, such mutant genes can be easily removed by ligating the gene with a commercially available activity expression vector, and measuring the phosphatase activity in accordance with, for example, the method of Lewis, I. Pizer (J. Biol. Chem., 238(12), 3934-3944(1963)).
It is preferred that the DNA of the present invention is ligated with vector DNA autonomously replicable in cells of Escherichia coli and/or coryneform bacteria to prepare recombinant DNA, and the recombinant DNA is introduced into cells of Escherichia coli beforehand. Such provision makes following operations easy. The vector autonomously replicable in cells of Escherichia coli is preferably a plasmid vector which is preferably autonomously replicable in cells of a host, including, for example, pUC19, pUC18, pBR322, pHSG299, pHSG399, pHSG398, and RSF1010.
Recombinant DNA may be prepared by utilizing transposon (WO 02/02627 International Publication Pamphlet, WO 93/18151 International Publication Pamphlet, European Patent Application Laid-open No. 0445385, Japanese Patent Application Laid-open No. 6-46867, Vertes, A. A. et al., Mol. Microbiol., 11, 739-746 (1994), Bonamy, C., et al., Mol. Microbiol., 14, 571-581 (1994), Vertes, A. A. et al., Mol. Gen. Genet., 245, 397-405 (1994), Jagar, W. et al., FEMS Microbiology Letters, 126, 1-6 (1995), Japanese Patent Application Laid-open No. 7-107976, Japanese Patent Application Laid-open No. 7-327680, etc.), phage vectors, recombination of chromosomes (Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press (1972); Matsuyama, S. and Mizushima, S., J. Bacteriol., 162, 1196 (1985)) and the like.
When a DNA fragment having an ability to allow a plasmid to be autonomously replicable in coryneform bacteria is inserted into these vectors, they can be used as a so-called shuttle vector autonomously replicable in both Escherichia coli and coryneform bacteria.
Such a shuttle vector includes the followings. Microorganisms harboring each of vectors and deposition numbers in international deposition facilities are shown in parentheses.
pHC4: Escherichia coli AJ12617 (FERM BP-3532)
pAJ655: Escherichia coli AJ11882 (FERM BP-136),
Corynebacterium glutamicum SR8201 (ATCC 39135)
pAJ1844: Escherichia coli AJ11883 (FERM BP-137),
Corynebacterium glutamicum SR8202 (ATCC 39136)
pAJ611: Escherichia coli AJ11884 (FERM BP-138)
pAJ3148: Corynebacterium glutamicum SR8203 (ATCC 39137)
pAJ440: Bacillus subtilis AJ11901 (FERM BP-140)
These vectors are obtainable from the deposited microorganisms as follows. Cells collected at a logarithmic growth phase were lysed by using lysozyme and SDS, followed by separation from a lysate by centrifugation at 30,000xc3x97g to obtain a supernatant to which polyethylene glycol is added, followed by fractionation and purification by means of cesium chloride-ethidium bromide equilibrium density gradient centrifugation.
Escherichia coli can be transformed by introducing a plasmid in accordance with, for example, a method of D. A. Morrison (Methods in Enzymology, 68, 326 (1979)) or a method in which recipient cells are treated with calcium chloride to increase permeability for DNA (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)).
Introduction of plasmids to coryneform bacteria to cause transformation can he performed by the electric pulse method (Sugimoto et al., Japanese Patent Application Laid-open No. 2-207791).
The phosphoserine phosphatase can be produced by expressing the DNA of the present invention using a suitable host-vector system.
As a host for the expression of the DNA of the present invention, various prokaryotic cells including bacteria belonging to the Corynebacterium such as Brevibacterium flavum, Escherichia coli, Bacillus subtilis, various eukaryotic cells including Saccharomyces cerevisiae, animal cells, and plant cells can be mentioned. Among these, prokaryotic cells, in particular, Escherichia coli and Bacillus subtilis are preferred.
Since the DNA of the present invention does not have a promoter, in order to express the gene it requires that a promoter which functions in the host cell, such as lac, trp and PL is ligated to the upstream of the DNA sequence. By utilizing a vector containing a promoter as the vector, the ligation of the gene to both vector and promoter can be performed by one step. As such a vector, pMW219 containing lacZ promoter (available from Nippon gene) can be mentioned.
When the DNA is highly expressed, the plasmid containing the DNA of the present invention occasionally becomes unstably. In that case, low copy vector is preferable.
The transformation can be attained by, for example, the method in which recipient cells are treated with calcium chloride to increase permeability for DNA as reported for Escherichia coli K-12 strain (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)), or the method utilizing introduction of DNA into competent cells produced from cells at a growth phase as reported for Bacillus subtilis (Duncan, C. H., Wilson, G. A., and Young, F. E., Gene, 1, 153 (1977)). It is also possible to prepare a protoplast or spheroplast of DNA recipient cell, which readily incorporates DNA, and introduce DNA into it as known for Bacillus subtilis, Actinomycetes and yeast (Changs, S. and Choen, S. N., Molec. Gen. Genet., 168, 111 (1979); Bibb, M. J., Ward, J. M. and Hopwood, O. A., Nature, 274, 398 (1978); Hinnen, A., Hicks, J. B., and Fink, G. R., Proc. Natl. Acad. Sci. USA, 75, 1929 (1978)). Electric pulse method is also effective for coryneform bacteria (Japanese Patent Application Laid-open No. 2-207791). The method can be suitably selected from these depending on the cell to be used as the host.
The phosphoserine phosphatase can be produced by culturing cells to which the DNA of the present invention is introduced in such a manner that the DNA can be expressed as described above in a medium to produce and accumulate phosphoserine phosphatase in the culture, and collecting the phosphoserine phosphatase from the culture. The culture medium can be selected according to the host to be used.
The phosphoserine phosphatase produced as described above can be purified from a cell extract or medium as required by using a usual purification method for enzymes, for example, ion exchange chromatography, gel filtration chromatography, adsorption chromatography, solvent precipitation and the like.
Further, the DNA of present invention may be utilized for breeding L-serine producing bacteria belonging to coryneform bacteria or the like. That is, by conferring or enhancing phosphoserine phosphatase activity by introducing the DNA of present invention into bacterium in a form that the DNA can be expressed, L-serine productivity is conferred and enhanced. Moreover, enhancement of phosphoserine phosphatase activity can be also performed by amplifying copy numbers of serB homologue and modifying expression control sequence in order to enhance expression of serB homologue in chromosome of Brevibacterium flavum. Modification of expression control sequence in chromosomal DNA is performed by, for exsample, substituting strong expression control sequence such as promoter and the like for that of the operon containing serB homologue (Japanese Patent Application Laid-open No. 1-215280).
Examples of the coryneform bacterium may be used for breeding L-amino acid producing bacteria include, for example, the following wild type strains:
Corynebacterium acetoacidophilum ATCC 13870;
Corynebacterium acetoglutamicum ATCC 15806;
Corynebacterium callunae ATCC 15991;
Corynebacterium glutamicum ATCC 13032;
(Brevibacterium divaricatum) ATCC 14020;
(Brevibacterium lactofermentum) ATCC 13869;
(Corynebacterium lilium) ATCC 15990;
Brevibacterium flavum ATCC 14067;
Corynebacterium melassecola ATCC 17965;
Brevibacterium saccharolyticum ATCC 14066;
Brevibacterium immariophilum ATCC 14068;
Brevibacterium roseum ATCC 13825;
Brevibacterium thiogenitalis ATCC 19240;
Microbacterium ammoniaphilum ATCC 15354;
Corynebacterium thermoaminogenes AJ12340 (FERM BP-1539).
Mutant strain having resistance to azaserine or xc3xa2-(2-chenyl)-DL-alanine (European Patent Publication No. 943,687) may be also utilized for breeding L-serine producing bacteria as a starting strain.
Further, the DNA of present invention may be introduced into L-serine producing bacteria with other genes of enzyme involving L-serine biosynthesis. Such genes include the gene coding for D-3-phosphoglyceratedehydrogenase (serA) (European Patent Publication No. 943,687), phosphoserinephosphatase (serB) and phosphoserinetransaminase (serC) (European Patent Publication No. 931,833). As serA, mutant gene coding for D-3-phosphoglyceratedehydrogenase whose feedback inhibition by L-serine is desensitized (European Patent Publication No. 943,687).
L-serine may be produced directly from sugars by culturing the microorganisms to which the DNA of the present invention is introduced in such a form that the DNA can be expressed and which have L-serine producing ability in a medium to accumulate L-serine in the midium and collecting L-serine from the medium. Further, the microorganisms to which the DNA of the present invention is introduced may be applied for a method producing L-serine utilizing L-serine precursor such as glycine and the like, so long as phosphoserine phosphatase is involved in the method.
For L-serine production using the microorganisms to which the DNA of the present invention, the following medium may be used. There can be used conventional liquid media containing carbon sources, nitrogen sources, inorganic salts, and optionally organic trace nutrients such as amino acids, vitamins, etc., if desired.
As carbon sources, it is possible to use sugars such as glucose, sucrose, fructose, galactose; saccharified starch solutions, sweet potato molasses, sugar beet molasses and hightest molasses which are including the sugars described above; organic acids such as acetic acid; alcohols such as ethanol; glycerol and the like.
As nitrogen sources, it is possible to use ammonia gas, aqueous ammonia, ammonium salts, urea, nitrates and the like. Further, organic nitrogen sources for supplemental use, for example, oil cakes, soybean hydrolysate liquids, decomposed casein, other amino acids, corn steep liquor, yeast or yeast extract, peptides such as peptone, and the like, may be used.
As inorganic ions, phosphoric ion, magnesium ion, calcium ion, iron ion, manganese ion and the like may be added optionally.
In case of using the microorganism of the present invention which requires nutrients such as amino acids for its growth, the required nutrients should be supplemented.
The microorganisms are incubated usually under aerobic conditions at pH 5 to 8 and temperature ranges of 25 to 40 xc2x0 C. The pH of the culture medium is controlled at a predetermined value within the above-described ranges depending on the presence or absence of inorganic or organic acids, alkaline substances, urea, calcium carbonate, ammonia gas, and the like. L-Serine can be collected from the fermentation liquid, for example, by separating and removing the cells, subjecting to ion exchange resin treatment, concentration cooling crystallization, membrane separation, and other known methods in any suitable combination. In order to remove impurities, activated carbon adsorption and recrystallization may be used for purification.